[phenixbb] phenix.refine crash -- other error

Petrus H Zwart PHZwart at lbl.gov
Mon Mar 19 11:13:56 PDT 2007


Hi Ulrich,

As far as I understand, you have solved the problem by sourcing the proper version of cci_apps.

The files you send me look (actually glancing)  fine and were not the issue.

Cheers

Peter




----- Original Message -----
From: Ulrich Baumann <ulrich.baumann at ibc.unibe.ch>
Date: Monday, March 19, 2007 9:29 am
Subject: Re: [phenixbb] phenix.refine crash -- other error
To: PHENIX user mailing list <phenixbb at phenix-online.org>

> Files are attached -- hope I got the right ones....
> 
> Quoting Petrus H Zwart <PHZwart at lbl.gov>:
> 
> > This is very surprising. Not sure what happens actually.
> > 
> > Can you please go to the directory where you have the cci_apps 
> sources> located, specifically, this file:
> > 
> > /usr/local/cci_apps/cci_apps_sources/cctbx/cctbx/crystal/__init__.py
> > 
> > and grep for 
> > 
> > select_crystal_symmetry
> > 
> > Can you send me the build tag/version of cci_apps you installed? 
> That might
> > make it easier for me to find out exactly what is going on ...
> > 
> > or send me these files:
> > /usr/local/cci_apps/cci_apps_sources/cctbx/cctbx/crystal/__init__.py
> > /usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/examples/reindex.py
> > 
> > Sorry for this,
> > 
> > Peter
> > 
> > 
> > 
> > 
> > 
> > ----- Original Message -----
> > From: Ulrich Baumann <ulrich.baumann at ibc.unibe.ch>
> > Date: Friday, March 16, 2007 4:15 am
> > Subject: Re: [phenixbb] phenix.refine crash -- other error
> > To: PHENIX user mailing list <phenixbb at phenix-online.org>
> > 
> > > Hi Peter,
> > > 
> > > I hate to bother you guys with this but ....
> > > 
> > > dcb-macbeth:[lip3] > phenix.python
> > > 
> /usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/examples/reindex.py> > data.file=lip_r3_1.8A.mtz model.file=in.pdb action=reindex 
> > > standard_laws=niggli#phil __OFF__
> > > =================
> > >    REINDEX      
> > > A reindexing tool
> > > =================
> > > 
> > > Traceback (most recent call last):
> > >  File 
> > > 
> "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/examples/reindex.py",line> 468, in ?
> > >    reindex_utils(sys.argv[1:])
> > >  File 
> > > 
> "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/examples/reindex.py",line> 260, in reindex_utils
> > >    combined_xs = crystal.select_crystal_symmetry(
> > > AttributeError: 'module' object has no attribute 
> > > 'select_crystal_symmetry'
> > > 
> > > I seem to hae to set a spacegroup? Sorry, I could not find a 
> > > documentation for
> > > the reindex utility.
> > > 
> > > Many thanks,
> > > 
> > > Ulrich
> > > 
> > > Quoting Peter Zwart <PHZwart at lbl.gov>:
> > > 
> > > > Hi Ulrich,
> > > > 
> > > > You could try refining your structure in a primitive setting, 
> > > this might 
> > > >   alleviate memory usage a bit (not sure though).
> > > > 
> > > > try
> > > > 
> > > > phenix.python $MMTBX_DIST/mmtbx/examples/reindex.py 
> > > data.file=mydata.mtz 
> > > >   model.file=mymodel.pdb action=reindex standard_laws=niggli
> > > > 
> > > > You will get a new mtz file and a new pdb file. 
> Unfortunately, 
> > > the free 
> > > > flags are not copied over, so you would have to reindex those 
> > > separately 
> > > > using iotbx.reflection_file_converter and read that file in 
> > > separately 
> > > > in phenix.refine.
> > > > 
> > > > This might be a bit criptic, if so, let me know and I will 
> post 
> > > more 
> > > > details.
> > > > 
> > > > I am not sure this does the trick though, I hope Ralf or 
> Pavel 
> > > can give 
> > > > some suggestions.
> > > > 
> > > > Cheers
> > > > 
> > > > Peter
> > > > 
> > > > 
> > > > 
> > > > 
> > > > Ulrich Baumann wrote:
> > > > > Hi there,
> > > > > 
> > > > > if you remove the ANISOU card from the input pdb file, 
> phenix 
> > > will run
> > > > fine
> > > > > ....sometimes not.
> > > > > 
> > > > > phenix.refine ( Version: 2007_01_24_2154) crashed for me as 
> > > well: we have
> > > > a
> > > > > rather large unit cell and good resolution. The program 
> crashes> > > reproducibly
> > > > > (see below) when using resolution limits better than 3 A, 
> although> > > sometimes
> > > > > this only occurs in the 2nd macrocycle.
> > > > > 
> > > > > Working crystal symmetry after inspecting all inputs:
> > > > >   Unit cell: (202.401, 202.401, 317.731, 90, 90, 120)
> > > > >   Space group: R 3 :H (No. 146)
> > > > > 
> > > > > 
> > > > > We have 2 GB memory and could stuff in more but maybe we 
> can 
> > > limit the
> > > > memeory
> > > > > use in a different way?
> > > > > 
> > > > > 
> > > > > Thanks a lot for your help,
> > > > > 
> > > > > Ulrich
> > > > > 
> > > > > 
> > > > > ============================= ml refinement start
> > > > =============================
> > > > > 
> > > > > 
> > > > >    ----------structure factors based statistics (before
> > > > refinement)----------  
> > > > > 
> > > > > Traceback (most recent call last):
> > > > >   File
> > > > 
> > > 
> "/usr/local/cci_apps/cci_apps_sources/phenix/phenix/command_line/refine.p>> > y", line 5, in <module>
> > > > >     command_line.run(command_name="phenix.refine", 
> > > args=sys.argv[1:])> >   File
> > > > 
> > > 
> "/usr/local/cci_apps/cci_apps_sources/phenix/phenix/refinement/command_li>> > ne.py", line 75, in run
> > > > >     
> > > 
> call_back_after_monitor_collect=call_back_after_monitor_collect)> 
> > > >   File
> > > > 
> > > 
> "/usr/local/cci_apps/cci_apps_sources/phenix/phenix/refinement/driver.py">> > , line 1108, in run
> > > > >     log                     = log)
> > > > >   File
> > > > 
> > > 
> "/usr/local/cci_apps/cci_apps_sources/phenix/phenix/refinement/strategies>> > .py", line 174, in refinement_machine
> > > > >     abcd              = abcd)
> > > > >   File 
> > > "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/f_model.py", 
> line> > > 185, 
> > > > > in __init__
> > > > >     b_cart               = b_cart)
> > > > >   File 
> > > "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/f_model.py", 
> line> > > 466, 
> > > > > in update_xray_structure
> > > > >     f_mask = 
> bulk_solvent_mask_obj.structure_factors(miller_set=> > > self.f_obs)
> > > > >   File 
> > > "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/masks.py", line
> > > > 97, in 
> > > > > structure_factors
> > > > >     
> > > 
> flex.grid(fft_manager.m_real()).set_focus(fft_manager.n_real()))> 
> > > > MemoryError
> > > > > 
> > > > > ----------------------------------------------------------
> > > > > -------------------------------------------------------
> > > > > Quoting Pavel Afonine <pafonine at lbl.gov>:
> > > > > 
> > > > >> Hi,
> > > > >>
> > > > >> this is known problem and it will be fixed ASAP; sorry for 
> this.> > > >> This presumably happens because an atom selected to 
> be 
> > > refined as 
> > > > >> individual anisotropic is included into a TLS group.
> > > > >> I will let you know once the fixed version of CCI Apps is 
> > > available.> >>
> > > > >> Pavel.
> > > > >>
> > > > >>
> > > > >>
> > > > >> Jianghai Zhu wrote:
> > > > >>> Hi,
> > > > >>>
> > > > >>> I was using phenix.refine from the latest cci apps bundle 
> to 
> > > do 
> > > > >>> tls+individual_sites+individual_adp refinement.  The 
> program 
> > > crashed 
> > > > >>> with the following error message.
> > > > >>>
> > > > >>>              ----------Target weights (before refinement)-
> ---
> > > ------    
> > > > >>>        
> > > > >>>
> > > > >>> Traceback (most recent call last):
> > > > >>>   File 
> > > > >>> 
> > > 
> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/command_line/refine.py", 
> > > > >>> line 5, in <module>
> > > > >>>     command_line.run(command_name="phenix.refine", 
> > > args=sys.argv[1:])> >>>   File 
> > > > >>>
> > > > 
> > >
> > 
> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/command_line.py",>> >>> line 75, in run
> > > > >>>     
> > > 
> call_back_after_monitor_collect=call_back_after_monitor_collect)> 
> > > >>>   File 
> > > > >>> 
> > > 
> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/driver.py", 
> > > > >>> line 1108, in run
> > > > >>>     log                     = log)
> > > > >>>   File 
> > > > >>> 
> > > 
> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/strategies.py",>> 
> > > > >>> line 245, in refinement_machine
> > > > >>>     log                           = log)
> > > > >>>   File 
> > > > >>>
> > > > >>
> > > > 
> > >
> > 
> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/weight_xray_chem.py",>> >>
> > > > >>> line 222, in __init__
> > > > >>>     compute_gradients = True)
> > > > >>>   File 
> > > "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/restraints.py", 
> > > > >>> line 144, in energies_adp_aniso
> > > > >>>     xray_structure = xray_structure,
> > > > >>>   File 
> > > > >>> 
> > > 
> "/nfs/home/jzhu/cci_apps_sources/cctbx/cctbx/adp_restraints/__init__.py",>> 
> > > > >>> line 109, in __init__
> > > > >>>     self.check_flags(fl_i)
> > > > >>>   File 
> > > > >>> 
> > > 
> "/nfs/home/jzhu/cci_apps_sources/cctbx/cctbx/adp_restraints/__init__.py",>> 
> > > > >>> line 177, in check_flags
> > > > >>>     assert not fl.use_u_aniso()
> > > > >>> AssertionError
> > > > >>>
> > > > >>> Anyone has any idea what is happening?  Thanks.
> > > > >>>
> > > > >>> Jianghai
> > > > >>>
> > > > >>> +++++++++++++++++++++++++++++++
> > > > >>> Jianghai Zhu, Ph.D
> > > > >>> CBR Institute for Biomedical Research
> > > > >>> Department of Pathology
> > > > >>> Harvard Medical School
> > > > >>> 200 Longwood Ave., Boston, MA 02115
> > > > >>> Ph: 617-278-3211
> > > > >>> Fx: 618-278-3232
> > > > >>> +++++++++++++++++++++++++++++++
> > > > >>>
> > > > >>>
> > > > >>>
> > > > >>> ----------------------------------------------------------
> ---
> > > -----------
> > > > >>>
> > > > >>> _______________________________________________
> > > > >>> phenixbb mailing list
> > > > >>> phenixbb at phenix-online.org
> > > > >>> http://www.phenix-online.org/mailman/listinfo/phenixbb
> > > > >>>   
> > > > > 
> > > > > 
> > > > _______________________________________________
> > > > phenixbb mailing list
> > > > phenixbb at phenix-online.org
> > > > http://www.phenix-online.org/mailman/listinfo/phenixbb
> > > > 
> > > 
> > > 
> > > -- 
> > > ========================================
> > > Ulrich Baumann
> > > University of Berne
> > > ulrich.baumann at ibc.unibe.ch
> > > phone + 41 31 631 4320/4343
> > > fax + 41 31 631 4887
> > > 
> > > ------------------------------------------------------
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> > > 
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> > 
> 
> 
> -- 
> ========================================
> Ulrich Baumann
> University of Berne
> ulrich.baumann at ibc.unibe.ch
> phone + 41 31 631 4320/4343
> fax + 41 31 631 4887
> 
> ------------------------------------------------------
> This mail was sent through IMP at http://mail.unibe.ch
> 



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